The Sydney barrister Jay Williams spent the weekend at the Manus Island detention centre taking evidence from 75 asylum seekers who claim their human rights have been violated – but his inquiry could be shut down by the Papua New Guinea government on Monday.

In an extraordinary stand-off between the country’s executive and judiciary, Williams’s snap inquiry was ordered on Friday by Justice David Cannings of the PNG supreme court. Earlier the PNG government had succeeded in winning a legal stay against the judge’s own almost-finished human rights investigation.

It emerged that the Australian government has backed the attempts by the PNG government to shut down the inquiries into the centre, which is entirely Australian-funded and houses 1310 asylum seekers transferred from Australia.

The PNG foreign minister, Rimbink Pato, has told Fairfax media the Australian government was consulted and strongly supported his decision to try to shut down the inquiry instigated by Cannings.

"It's a joint effort. We're the best judges in terms of what's happening on the ground but we're in concert because this is a partnership. We're together," he said.

He said Cannings was not complying with "proper processes under PNG law". PNG has also alleged Cannings is biased. On Friday PNG won a stay on the Cannings inquiry while it launches a supreme court appeal against his refusal to disqualify himself on the grounds of bias.

Cannings immediately instituted new proceedings to allow Williams to launch another inquiry and Williams spent the weekend taking affidavits from asylum seekers at the centre. The PNG government has indicated it intends to shut down this as well.

Daniel Webb, the director of legal advocacy at Australia’s Human Rights Advocacy Centre, who with Amnesty International had been given leave to participate in the court’s inquiry, said the court was investigating whether human rights, enshrined in PNG’s constitutional bill of rights, were being respected at the centre. If the court found violations it had broad powers to make orders to protect asylum seekers’ human rights.

“Australia has gone to great lengths and great expense to put these asylum seekers beyond the reach of the rule of law; this inquiry is about taking the rule of law to them,” he told Guardian Australia from Port Moresby on Sunday.

The dispute between the executive and the judiciary came as PNG’s prime minister, Peter O’Neill, revealed his country may not resettle asylum seekers found to be refugees as it had promised Australia’s former Labor government.

Labor sources said there was an understanding at the time that the Australian government would look for other countries in the region that might be willing to take some of the refugees from Manus Island but if this wasn’t possible they would all be resettled in PNG.

But at a news conference with Abbott on Friday O’Neill said PNG would not be able to resettle all of the refugees from Manus, even though he also said he believed most of the 1310 people on the remote island would be found not to be refugees and would be sent back to their home countries. None of the men have had their refugee status determined, although processing has begun and in some cases is understood to be at draft decision stage.

“Not all … We will take some, we will take as much as we can, we will also want all the other countries in the region, others in the Pacific, to extend their participation … We expect everybody to carry a certain burden, as we do,” O’Neill said on Friday.

On Saturday Abbott backed O’Neill’s view that most people in the centre would not be found to be refugees.

"There's a lot that we've seen which justifies that suspicion," he said.

Australia is now seeking other countries in the region to resettle refugees but has not said which ones. The former Australian foreign minister Bob Carr sought to send some asylum seekers to the Solomon Islands but that country’s prime minister, Gordon Darcy Lilo, said at the time he was not ready to consider the proposal.

The previous Solomons government had offered a remote island to Australia’s then prime minister, Julia Gillard, for asylum seekers when she was developing the so-called “Malaysia solution”.